libSBML Python API
5.10.0
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{comp}
comp Implementation of the “comp” package extention to the SBMLDocument construct.The CompSBMLDocumentPlugin class inherits from the SBMLDocumentPlugin class, and codifies the extentions to the SBMLDocument class defined in the SBML Level 3 Hierarchical Model Composition
package (“comp”). This extention allows multiple Model objects to be defined in a single SBMLDocument, stored in an optional child ListOfModelDefinitions object, as well as define references to Model objects in other files, stored in the optional child ListOfExternalModelDefinitions object. These model definitions, if present, allow Submodel objects to reference other Models to instantiate.
The presence of ModelDefinitions and ExternalModelDefinitions in an SBMLDocument does not change the default Model in the file. If a SBMLDocument is submitted somewhere to be simulated, it is still the <model>
child of the <sbml>
element that should be simulated.
In addition, as all packages do, the CompSBMLDocumentPlugin defines a required flag named required
, which indicates whether “comp” constructs can be used to change the core mathematics of the <model>
child of the <sbml>
element. Because they can, this attribute must be set True
.
Public Member Functions | |
def | addExternalModelDefinition |
def | addModelDefinition |
def | clone |
def | createExternalModelDefinition |
def | createModelDefinition |
def | getElementByMetaId |
def | getElementBySId |
def | getElementNamespace |
def | getExternalModelDefinition |
def | getLevel |
def | getListOfAllElements |
def | getListOfExternalModelDefinitions |
def | getListOfModelDefinitions |
def | getModel |
def | getModelDefinition |
def | getNumExternalModelDefinitions |
def | getNumModelDefinitions |
def | getPackageName |
def | getPackageVersion |
def | getParentSBMLObject |
def | getPrefix |
def | getRequired |
def | getSBMLDocument |
def | getURI |
def | getVersion |
def | isSetRequired |
def | removeExternalModelDefinition |
def | removeModelDefinition |
def | setElementNamespace |
def | setRequired |
def | unsetRequired |
def libsbml.CompSBMLDocumentPlugin.addExternalModelDefinition | ( | self, | |
args | |||
) |
Python method signature(s):
addExternalModelDefinition(CompSBMLDocumentPlugin self, ExternalModelDefinition externalModelDefinition)int
Adds a copy of the given ExternalModelDefinition object to the list of ExternalModelDefinitions.
externalModelDefinition | the ExternalModelDefinition object to be added to the list of ExternalModelDefinitions. Fails if the added ExternalModelDefinition is None , does not match the level/version/package of the parent object, or cannot be added to the list of external model definitions. |
def libsbml.CompSBMLDocumentPlugin.addModelDefinition | ( | self, | |
args | |||
) |
Python method signature(s):
addModelDefinition(CompSBMLDocumentPlugin self, ModelDefinition modelDefinition)int
Adds a copy of the given ModelDefinition object to the list of ModelDefinitions.
modelDefinition | the ModelDefinition object to be added to the list of ModelDefinitions. Fails if the added ModelDefinition is None , does not match the level/version/package of the parent object, or cannot be added to the list of replaced elements. |
def libsbml.CompSBMLDocumentPlugin.clone | ( | self | ) |
{comp}
comp Implementation of the “comp” package extention to the SBMLDocument construct.The CompSBMLDocumentPlugin class inherits from the SBMLDocumentPlugin class, and codifies the extentions to the SBMLDocument class defined in the SBML Level 3 Hierarchical Model Composition
package (“comp”). This extention allows multiple Model objects to be defined in a single SBMLDocument, stored in an optional child ListOfModelDefinitions object, as well as define references to Model objects in other files, stored in the optional child ListOfExternalModelDefinitions object. These model definitions, if present, allow Submodel objects to reference other Models to instantiate.
The presence of ModelDefinitions and ExternalModelDefinitions in an SBMLDocument does not change the default Model in the file. If a SBMLDocument is submitted somewhere to be simulated, it is still the <model>
child of the <sbml>
element that should be simulated.
In addition, as all packages do, the CompSBMLDocumentPlugin defines a required flag named required
, which indicates whether “comp” constructs can be used to change the core mathematics of the <model>
child of the <sbml>
element. Because they can, this attribute must be set True
. Python method signature(s):
clone(CompSBMLDocumentPlugin self)CompSBMLDocumentPlugin
Creates and returns a deep copy of this CompSBMLDocumentPlugin object.
def libsbml.CompSBMLDocumentPlugin.createExternalModelDefinition | ( | self | ) |
Python method signature(s):
createExternalModelDefinition(CompSBMLDocumentPlugin self)ExternalModelDefinition
Creates a ExternalModelDefinition object, adds it to the end of the ExternalModelDefinition objects list and returns a pointer to the newly created object.
def libsbml.CompSBMLDocumentPlugin.createModelDefinition | ( | self | ) |
Python method signature(s):
createModelDefinition(CompSBMLDocumentPlugin self)ModelDefinition
Creates a ModelDefinition object, adds it to the end of the ModelDefinition objects list and returns a pointer to the newly created object.
def libsbml.CompSBMLDocumentPlugin.getElementByMetaId | ( | self, | |
args | |||
) |
Python method signature(s):
getElementByMetaId(CompSBMLDocumentPlugin self, string metaid)SBase
Returns the first child element it can find with the given metaid
, or itself if it has the given metaid
, or None
if no such object is found.
metaid | string representing the meta identifier of objects to find |
metaid
. def libsbml.CompSBMLDocumentPlugin.getElementBySId | ( | self, | |
args | |||
) |
Python method signature(s):
getElementBySId(CompSBMLDocumentPlugin self, string id)SBase
Returns the first child element found that has the given id
in the model-wide SId namespace, or None
if no such object is found.
id | string representing the identifier of objects to find |
id
.
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inherited |
{core}
Representation of a plug-in object of SBML's package extension.Additional attributes and/or elements of a package extension which are directly contained by some pre-defined element are contained/accessed by SBasePlugin class which is extended by package developers for each extension point. The extension point, which represents an element to be extended, is identified by a combination of a Package name and a typecode of the element, and is represented by SBaseExtensionPoint class.
For example, the layout extension defines <listOfLayouts> element which is directly contained in <model> element of the core package. In the layout package (provided as one of example packages in libSBML-5), the additional element for the model element is implemented as ListOfLayouts class (an SBase derived class) and the object is contained/accessed by a LayoutModelPlugin class (an SBasePlugin derived class).
SBasePlugin class defines basic virtual functions for reading/writing/checking additional attributes and/or top-level elements which should or must be overridden by subclasses like SBase class and its derived classes.
Package developers must implement an SBasePlugin exntended class for each element to be extended (e.g. SBMLDocument, Model, ...) in which additional attributes and/or top-level elements of the package extension are directly contained.
To implement reading/writing functions for attributes and/or top-level elements of the SBsaePlugin extended class, package developers should or must override the corresponding virtual functions below provided in the SBasePlugin class:
reading elements :
virtual SBase createObject (XMLInputStream stream)
This function must be overridden if one or more additional elements are defined.
virtual bool readOtherXML (SBase parentObject, XMLInputStream stream)
This function should be overridden if elements of annotation, notes, MathML, etc. need to be directly parsed from the given XMLInputStream object.
reading attributes (must be overridden if additional attributes are defined) :
virtual void addExpectedAttributes(ExpectedAttributes& attributes)
virtual void readAttributes (XMLAttributes attributes, ExpectedAttributes& expectedAttributes)
writing elements (must be overridden if additional elements are defined) :
virtual void writeElements (XMLOutputStream stream)
writing attributes :
virtual void writeAttributes (XMLOutputStream stream)
This function must be overridden if one or more additional attributes are defined.
virtual void writeXMLNS (XMLOutputStream stream)
This function must be overridden if one or more additional xmlns attributes are defined.
checking elements (should be overridden) :
virtual bool hasRequiredElements()
checking attributes (should be overridden) :
virtual bool hasRequiredAttributes()
To implement package-specific creating/getting/manipulating functions of the SBasePlugin derived class (e.g., getListOfLayouts(), createLyout(), getLayout(), and etc are implemented in LayoutModelPlugin class of the layout package), package developers must newly implement such functions (as they like) in the derived class.
SBasePlugin class defines other virtual functions of internal implementations such as:
virtual void setSBMLDocument(SBMLDocument d)
virtual void connectToParent(SBasesbase)
virtual void enablePackageInternal(string pkgURI, string pkgPrefix, bool flag)
These functions must be overridden by subclasses in which one or more top-level elements are defined.
For example, the following three SBasePlugin extended classes are implemented in the layout extension:
SBMLDocumentPlugin class for SBMLDocument element
(SBMLDocumentPlugin class is a common SBasePlugin extended class for SBMLDocument class. Package developers can use this class as-is if no additional elements/attributes (except for required attribute) is needed for the SBMLDocument class in their packages, otherwise package developers must implement a new SBMLDocumentPlugin derived class.)
LayoutModelPlugin class for Model element
<listOfLayouts> element is added to Model object.
The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)
createObject()
: (read elements) readOtherXML()
: (read elements in annotation of SBML L2) writeElements()
: (write elements) The following virtual functions of internal implementations are overridden: (type of arguments and return values are omitted)
setSBMLDocument()
connectToParent()
enablePackageInternal()
The following creating/getting/manipulating functions are newly implemented: (type of arguments and return values are omitted)
getListOfLayouts()
getLayout ()
addLayout()
createLayout()
removeLayout()
getNumLayouts()
LayoutSpeciesReferencePlugin class for SpeciesReference element (used only for SBML L2V1)
id attribute is internally added to SpeciesReference object only for SBML L2V1
The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)
readOtherXML()
writeAttributes()
Python method signature(s):
getElementNamespace(SBasePlugin self)string
Returns the XML namespace (URI) of the package extension of this plugin object.
def libsbml.CompSBMLDocumentPlugin.getExternalModelDefinition | ( | self, | |
args | |||
) |
Python method signature(s):
getExternalModelDefinition(CompSBMLDocumentPlugin self, long n)ExternalModelDefinition getExternalModelDefinition(CompSBMLDocumentPlugin self, long n)
ExternalModelDefinition getExternalModelDefinition(CompSBMLDocumentPlugin self, string sid)
ExternalModelDefinition getExternalModelDefinition(CompSBMLDocumentPlugin self, string sid)
ExternalModelDefinition
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
getExternalModelDefinition(long n)
Returns the ExternalModelDefinition with the given index.
n | the index number of the ExternalModelDefinition to get. |
None
is returned.getExternalModelDefinition(string sid)
Returns the model definition object based on its identifier.
sid | a string representing the identifier of the model definition to get. |
sid
or None
if no such ExternalModelDefinition exists.
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inherited |
Python method signature(s):
getLevel(SBasePlugin self)long
Returns the SBML level of the package extension of this plugin object.
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inherited |
def libsbml.CompSBMLDocumentPlugin.getListOfExternalModelDefinitions | ( | self | ) |
Python method signature(s):
getListOfExternalModelDefinitions(CompSBMLDocumentPlugin self)ListOfExternalModelDefinitions
Returns the ListOf object that holds all ExternalModelDefinitions.
def libsbml.CompSBMLDocumentPlugin.getListOfModelDefinitions | ( | self | ) |
Python method signature(s):
getListOfModelDefinitions(CompSBMLDocumentPlugin self)ListOfModelDefinitions
Returns the ListOf object that holds all ModelDefinitions.
def libsbml.CompSBMLDocumentPlugin.getModel | ( | self, | |
args | |||
) |
Python method signature(s):
getModel(CompSBMLDocumentPlugin self, string sid)SBase getModel(CompSBMLDocumentPlugin self, string sid)
SBase
Searches the model namespace of the document and returns the Model, ModelDefinition, or ExternalModelDefintion object with the given identifier.
sid | a string representing the identifier of the model definition to get. |
sid
or None
if no such model exists. If no such model exists, this will return None
. def libsbml.CompSBMLDocumentPlugin.getModelDefinition | ( | self, | |
args | |||
) |
Python method signature(s):
getModelDefinition(CompSBMLDocumentPlugin self, long n)ModelDefinition getModelDefinition(CompSBMLDocumentPlugin self, long n)
ModelDefinition getModelDefinition(CompSBMLDocumentPlugin self, string sid)
ModelDefinition getModelDefinition(CompSBMLDocumentPlugin self, string sid)
ModelDefinition
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
getModelDefinition(long n)
Returns the ModelDefinition with the given index.
n | the index number of the ModelDefinition to get. |
n
is invalid, None
is returned.getModelDefinition(string sid)
Returns the model definition object based on its identifier.
sid | a string representing the identifier of the model definition to get. |
sid
or None
if no such ModelDefinition exists.def libsbml.CompSBMLDocumentPlugin.getNumExternalModelDefinitions | ( | self | ) |
Python method signature(s):
getNumExternalModelDefinitions(CompSBMLDocumentPlugin self)long
Returns the number of ExternalModelDefinitions for this SBMLDocumentPlugin.
def libsbml.CompSBMLDocumentPlugin.getNumModelDefinitions | ( | self | ) |
Python method signature(s):
getNumModelDefinitions(CompSBMLDocumentPlugin self)long
Returns the number of ModelDefinitions for this SBMLDocumentPlugin.
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inherited |
Python method signature(s):
getPackageName(SBasePlugin self)string
Returns the package name of this plugin object.
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inherited |
Python method signature(s):
getPackageVersion(SBasePlugin self)long
Returns the package version of the package extension of this plugin object.
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inherited |
Python method signature(s):
getParentSBMLObject(SBasePlugin self)SBase getParentSBMLObject(SBasePlugin self)
SBase
Returns the parent SBase object to which this plugin object connected.
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inherited |
Python method signature(s):
getPrefix(SBasePlugin self)string
Returns the prefix of the package extension of this plugin object.
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inherited |
Python method signature(s):
getRequired(SBMLDocumentPlugin self)bool
Returns the bool value of 'required' attribute of corresponding package in SBMLDocument element.
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inherited |
Python method signature(s):
getSBMLDocument(SBasePlugin self)SBMLDocument getSBMLDocument(SBasePlugin self)
SBMLDocument
Returns the parent SBMLDocument of this plugin object.
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inherited |
Python method signature(s):
getURI(SBasePlugin self)string
Gets the URI to which this element belongs to. For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'
Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. if not found it will return the result of getElementNamespace
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inherited |
Python method signature(s):
getVersion(SBasePlugin self)long
Returns the SBML version of the package extension of this plugin object.
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inherited |
Python method signature(s):
isSetRequired(SBMLDocumentPlugin self)bool
Predicate returning True
or False
depending on whether this SBMLDocumentPlugin's 'required' attribute has been set.
True
if the 'required' attribute of this SBMLDocument has been set, False
otherwise. def libsbml.CompSBMLDocumentPlugin.removeExternalModelDefinition | ( | self, | |
args | |||
) |
Python method signature(s):
removeExternalModelDefinition(CompSBMLDocumentPlugin self, long index)ExternalModelDefinition removeExternalModelDefinition(CompSBMLDocumentPlugin self, string id)
ExternalModelDefinition
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
removeExternalModelDefinition(string id)
Removes the ExternalModelDefinition with the given id
.
A pointer to the ExternalModelDefinition that was removed is returned. If no ExternalModelDefinition has been removed, None
is returned.
id | the id of the ExternalModelDefinition object to remove |
None
is returned if the given index is out of range.removeExternalModelDefinition(long index)
Removes the ExternalModelDefinition with the given index.
A pointer to the ExternalModelDefinition that was removed is returned. If no ExternalModelDefinition has been removed, None
is returned.
index | the index of the ExternalModelDefinition object to remove |
None
is returned if the given index is out of range. def libsbml.CompSBMLDocumentPlugin.removeModelDefinition | ( | self, | |
args | |||
) |
Python method signature(s):
removeModelDefinition(CompSBMLDocumentPlugin self, long index)ModelDefinition removeModelDefinition(CompSBMLDocumentPlugin self, string id)
ModelDefinition
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
removeModelDefinition(string id)
Removes the ModelDefinition with the given id
from the CompSBMLDocumentPlugin.
A pointer to the ModelDefinition that was removed is returned. If no ModelDefinition has been removed, None
is returned.
id | the id of the ModelDefinition object to remove |
None
is returned if the given index is out of range.removeModelDefinition(long index)
Removes the ModelDefinition with the given index from the CompSBMLDocumentPlugin.
A pointer to the ModelDefinition that was removed is returned. If no ModelDefinition has been removed, None
is returned.
index | the index of the ModelDefinition object to remove |
None
is returned if the given index is out of range.
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inherited |
Python method signature(s):
setElementNamespace(SBasePlugin self, string uri)int
Sets the XML namespace to which this element belongs to. For example, all elements that belong to SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/layout/version1/'
def libsbml.CompSBMLDocumentPlugin.setRequired | ( | self, | |
args | |||
) |
Python method signature(s):
setRequired(CompSBMLDocumentPlugin self, bool value)int
Sets the bool value of 'required' attribute of corresponding package in SBMLDocument element. The only legal value is 'true' for the Hierarchical Model Composition package.
value | the bool value of 'required' attribute of corresponding package in SBMLDocument element. |
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inherited |
Python method signature(s):
unsetRequired(SBMLDocumentPlugin self)int
Unsets the value of the 'required' attribute of this SBMLDocumentPlugin.